YANA – a software tool for analyzing flux modes, gene-expression and enzyme activities

BACKGROUND: A number of algorithms for steady state analysis of metabolic networks have been developed over the years. Of these, Elementary Mode Analysis (EMA) has proven especially useful. Despite its low user-friendliness, METATOOL as a reliable high-performance implementation of the algorithm has been the instrument of choice up to now. As reported here, the analysis of metabolic networks has been improved by an editor and analyzer of metabolic flux modes. Analysis routines for expression levels and the most central, well connected metabolites and their metabolic connections are of particular interest. RESULTS: YANA features a platform-independent, dedicated toolbox for metabolic networks with a graphical user interface to calculate (integrating METATOOL), edit (including support for the SBML format), visualize, centralize, and compare elementary flux modes. Further, YANA calculates expected flux distributions for a given Elementary Mode (EM) activity pattern and vice versa. Moreover, a dissection algorithm, a centralization algorithm, and an average diameter routine can be used to simplify and analyze complex networks. Proteomics or gene expression data give a rough indication of some individual enzyme activities, whereas the complete flux distribution in the network is often not known. As such data are noisy, YANA features a fast evolutionary algorithm (EA) for the prediction of EM activities with minimum error, including alerts for inconsistent experimental data. We offer the possibility to include further known constraints (e.g. growth constraints) in the EA calculation process. The redox metabolism around glutathione reductase serves as an illustration example. All software and documentation are available for download at . CONCLUSION: A graphical toolbox and an editor for METATOOL as well as a series of additional routines for metabolic network analyses constitute a new user-friendly software for such efforts

Epithelial Proinflammatory Response and Curcumin-Mediated Protection from Staphylococcal Toxic Shock Syndrome Toxin-1

Staphylococcus aureus initiates infections and produces virulence factors, including superantigens (SAgs), at mucosal surfaces. The SAg, Toxic Shock Syndrome Toxin-1 (TSST-1) induces cytokine secretion from epithelial cells, antigen presenting cells (APCs) and T lymphocytes, and causes toxic shock syndrome (TSS). This study investigated the mechanism of TSST-1-induced secretion of proinflammatory cytokines from human vaginal epithelial cells (HVECs) and determined if curcumin, an anti-inflammatory agent, could reduce TSST-1-mediated pathology in a rabbit vaginal model of TSS. TSST-1 caused a significant increase in NF-κB-dependent transcription in HVECs that was associated with increased expression of TNF- α, MIP-3α, IL-6 and IL-8. Curcumin, an antagonist of NF-κB-dependent transcription, inhibited IL-8 production from ex vivo porcine vaginal explants at nontoxic doses. In a rabbit model of TSS, co-administration of curcumin with TSST-1 intravaginally reduced lethality by 60% relative to 100% lethality in rabbits receiving TSST-1 alone. In addition, TNF-α was undetectable from serum or vaginal tissue of curcumin treated rabbits that survived. These data suggest that the inflammatory response induced at the mucosal surface by TSST-1 is NF-κB dependent. In addition, the ability of curcumin to prevent TSS in vivo by co-administration with TSST-1 intravaginally suggests that the vaginal mucosal proinflammatory response to TSST-1 is important in the progression of mTSS

Anwendung von Multireferenz-Methoden in der Chemie und Entwicklung eines Multireferenz Moller-Plesset-Störungstheorie-Programmes

The first part of this work focuses on the characterization of systems which complex electronic structures require the application of multi-reference methods. The anti-tumor efficacy of the natural product Neocarzinostatin is based on the formation of diradicals and causes DNA cleavage and finally cytolysis. Computations on model systems performed in the present work show the influence of structural features on the mode of action and the efficacy of this antitumor-antibiotic. The cyclization of systems related to the enyne-cumulene framework like the enyne-allenes was investigated earlier and relations to the more unusual class of enyne-ketenes are analyzed. The class of enyne-ketenes (and also the enyne-allenes) show a broad spectrum of possible intermediates (diradicals, zwitterions, allenes). The electronic structures of these intermediates are also possible for the (heteroatom substituted) 1,2,4-cyclohexatriene and a model for their energetic sequence based on high-level multi-reference computations is proposed. In all three projects the application of multi-reference approaches is necessary to obtain a comprehensive picture of the reactivity and electronic structure but also shows up the limits inherently existing in the currently available programs with respect to the size of the molecules. In the second part, algorithms for a multi-reference Moller-Plesset perturbation theory (MR-MP2) program, designed to perform large-scale computations, were developed and implemented. The MR-MP2 approach represents the most cost-effective multireference ansatz and requires an efficient evaluation of the Hamilton matrix for which an algorithm is designed to instantly recognize only non-vanishing matrix elements and to employ the recurring interaction patterns of the Hamilton matrix. The direct construction of the Hamilton matrix is additionally parallelized to work on cluster environments.Der erste Teil der vorliegenden Arbeit beschäftigt sich mit der Charakterisierung von Systemen, deren komplexe elektronische Struktur die Anwendung von Multireferenz-Methoden erfordert. Die Antitumor-Wirkung des Naturstoffes Neocarzinostatin beruht auf der Bildung von Diradikalen und führt zur Spaltung der DNS und löst den Zelltod aus. Berechnungen an Modellsystemen zeigen den Einfluss der Strukturmotive auf die Wirkungsweise und die Wirksamkeit des Antitumor-Antibiotikums. Die Cyclisierung von Systemen, wie die Eninallene, die dem Enincumulen-Grundgerüst des aktivierten Neocarzinostatin-Chromophors verwandt sind, wurden schon in früheren Arbeiten untersucht und die Verwandtschaft zur ungewöhnlicheren Substanzklasse der Eninketene wird in dieser Arbeit analysiert. Diese Verbindungsklasse und die der Eninallene zeigen ein breites Spektrum an möglichen Intermediaten, wie Diradikale, Carbene, Zwitterionen und Allene, deren elektronische Strukturen auch bei (heterosubstituierten) 1,2,4 Cyclohexatrienen auftreten. Für diese Verbindungen wird ein Modell für die energetische Abfolge der elektronischen Strukturen auf Basis von hochwertigen Multireferenz-Rechnungen vorgeschlagen. In den drei aufgeführten Projekten ist die Anwendung von Multireferenz-Ansätzen notwendig um ein umfassendes Bild der Reaktivitäten und elektronischen Strukturen zu erhalten, zeigen im Hinblick auf große Moleküle aber auch die inhärenten Grenzen in den zur Zeit verfügbaren Programme auf. Im zweiten Teil der Arbeit wurden Algorithmen für ein Multireferenz-Moller-Plesset-Störungstheorie-Programmes (MR-MP2) entwickelt und implementiert. Der MR-MP2-Ansatz stellt den effizientesten Multireferenz-Ansatz dar und setzt eine geschickte und schnelle Berechnung der Hamilton-Matrix voraus. Hierfür ist ein Algorithmus konzipiert worden, der zum einen verschwindende Matrixelemente sofort erkennt und die sich wiederholenden Muster innerhalb der Hamilton-Matrix zu Nutze macht. Die Konstruktion der Hamilton-Matrix für das direkte Verfahren ist zudem für Clusterumgebungen parallelisiert

The resonant step frequency in human running

At running speeds less than about 13 km h(-1) the freely chosen step frequency (f(free)) is lower than the frequency at which the mechanical power is minimized (f(min)). This dissociation between f(free) and f(min) was investigated by measuring mechanical power, metabolic energy expenditure and apparent natural frequency of the body's bouncing system (f(sist)) during running at three given speeds with different step frequencies. The f(free) requires a mechanical power greater than that at f(min) mainly due to a larger vertical oscillation of the body at each step. Energy expenditure is minimal and the mechanical efficiency is maximal at f(free). At a given speed, an increase in step frequency above f(free) results in an increase in energy expenditure despite a decrease in mechanical power. On the other hand, a decrease in step frequency below f(free) results in a larger increase in energy expenditure associated with an increase in mechanical power. When the step frequency is forced to values above or below f(free) f(sist) is forced to change similarly by adjusting the stiffness of the bouncing system. However the best match between f(sist) and step frequency takes place only in proximity of f(free) (2.6-2.8 Hz). It is concluded that during running at speeds less than 13 km h(-1) energy is saved by tuning step frequency to f(sist), even if this requires a mechanical power larger than necessary

Evaluation et homologation de variétés issues des vergers à graines de l'Etat - Programme 2011. Rapport final

This report shows the work done in 2011 by Irstea, INRA, ONF and CNPF in the framework of a research programme dedicated to improved varieties testing. It includes six species (Douglas-fir, larch, Black and Scots pines, wild cherry, ash) and a transversal topic (remote detection). With regard to Douglas-fir, the four partners continued the establishment of a network of comparative trials including the 8 French seed orchards and a control from the natural range. With two new trials, the network is now composed of 17 experimental plots and 10 demonstration plots. On the whole, survival is satisfactory. Most of the improved varieties show a better initial growth than the control. Still, the Californian variety is characterised by a slow growth in every site. Moreover, all the orchards have been ranked for timing of bud flushing. Ranking the varieties for cold hardiness in autumn will be the next step. Research has begun in 2011 in that respect. In larch, INRA studied the interest of IR spectrométry for larch taxa identification. The results obtained in 2011 on needles are encouraging. Furthermore, Irstea analysed the performances of hybrids and pure species individuals in the progenies of four "hybrid" varieties. Simulated thinnings show that the stand will become richer in hybrids if the trees are selected for growth. However, the final percentage of hybrid will depend on the variety. On the other hand, hybrid percentage will remain the same if the preference is given to stem form. Concerning remote sensing, Irstea work has focused on image segmentation. Several experimental plots and orchards have been analysed.Ce compte rendu d'activité présente les actions entreprises de mars 2011 à mars 2012 par Irstea, l'INRA, l'ONF et le CNPF dans le cadre de l'évaluation des variétés issues des vergers à graines de l'Etat. Elles concernent 6 espèces – Douglas, mélèzes, pins laricio et sylvestre, merisier, frêne – et un thème transversal qui consiste à identifier des techniques susceptibles de caractériser l'état physiologique des arbres de différentes espèces/provenances. Dans un premier temps, l'accent est mis sur les applications possibles de la télédétection. Pour ce qui concerne le Douglas, les quatre partenaires se sont mobilisés pour mettre en pace un réseau national de dispositifs destiné à évaluer les performances des 8 vergers de Douglas français. En 2011, le réseau s'est enrichi de deux nouveaux essais plantés au printemps dans le coeur de l'aire et en altitude. Il est à présent constitué de 17 dispositifs d'évaluation et 10 tests de démonstration. En outre, deux dispositifs comparant les variétés La Luzette et Californie, pures et en mélange, auront été installés. Dans l'ensemble, l'état des dispositifs est satisfaisant puisque 24 d'entre eux ont une mortalité inférieure à 20%. On déplore néanmoins la perte de deux tests. Des mesures de hauteur ont été prises régulièrement dans la majorité des sites. La variété californienne se caractérise par une faible vigueur initiale dans tous les milieux. Si l'on excepte Darrington, relativement peu vigoureuse, les autres variétés ont généralement une croissance supérieure au témoin de l'aire naturelle (seed zone Washington 403). Les notations de débourrement confirment la hiérarchie établie l'année précédente et, surtout, permettent de classer le verger Washington par rapport aux 7 autres vergers français. En définitive, 4 vergers de l'Etat apportent une amélioration sur ce caractère par rapport au témoin Washington 403 : Washington 2, La Luzette, Washington et, à un degré moindre, Darrington. Concernant la résistance au froid, l'enjeu est maintenant de classer les vergers pour l'aoûtement à l'automne. Une étude bibliographique a été faite dans cette perspective. En outre, Irstea a aménagé une serre de manière à conduire des essais en conditions semi-contrôlées. Des plants issus des vergers La Luzette et Californie ont été installés dans des caisses métalliques et seront soumis à trois ambiances climatiques en 2012. D'autre part, des mesures indirectes de densité du bois ont été prises par l'INRA dans deux tests de descendances du verger Darrington. En moyenne, les familles sont proches de la provenance Sauk River, originaire de la seed zone 403 (Etat du Washington) pour la densité du bois et la vigueur. Malgré des différences nettes entre moyennes familiales, une amélioration significative des performances du verger Darrington ne pourrait s'envisager que par une éclaircie vigoureuse, réduisant fortement la base génétique du verger qui est déjà limitée. Pour le mélèze, l'INRA a étudié le potentiel de la spectrométrie infra-rouge pour identifier les différents taxa de mélèze. Les travaux réalisés en 2011sur aiguilles sont encourageants. De plus, Irstea a analysé les performances des individus hybrides et d'espèces pures de quatre variétés "hybrides" implantées dans un dispositif du Limousin. Les simulations d’éclaircies montrent que la plantation s’enrichit en hybrides si on met l’accent sur la production de bois mais que le taux d’hybrides évolue peu si l’on privilégie la forme. En définitive, l'impact du taux d'hybrides dans les MFR dépend de deux facteurs : la stratégie du propriétaire (objectif vigueur ou forme) et la variété considérée (différentiel de croissance entre hybrides et espèces pures). En matière de télédétection, les travaux d'Irstea se sont concentrés sur la segmentation d’images afin de tirer le meilleur parti des photographies aériennes prises en 2009 au-dessus de plusieurs dispositifs expérimentaux et vergers à graines

Long-term and large-scale Quercus petraea population survey conducted in provenance tests installed in France

Provenance tests are invaluable resources in forest genetics and ecology. They were originally established for seed sourcing research, but they are now also used for monitoring and predicting population responses to environmental changes. They have also raised considerable interest for conservation purposes. We provide here a data resource for a multisite large-scale long-term provenance test on sessile oak (Quercus petraea (Matt.) Liebl.) setup in the late 1980s in France, supplemented with a few selected Q. robur provenances. The experimental layout comprises a range-wide collection of 124 provenances (109 Q. petraea and 15 Q. robur) planted at four experimental sites covering 90 ha in total. The dataset includes individual tree assessments of traits of functional, ecological and economic importance

Provenance variation and seed sourcing for sessile oak (Quercus petraea (Matt.) Liebl.) in France

Sessile oak (Quercus petraea (Matt.) Liebl.) provenance variation was assessed in a multisite test based on traits of economic and ecological relevance in France. While climatic drivers generated genetic clines at a range-wide scale, provenance variation in France was mainly shaped by past silvicultural regimes. We developed a multitrait approach to facilitate decision-making for seed sourcing. A set of provenance clusters is proposed, supporting recommendations for plantation programmes. Context Among broadleaves, sessile oak (Quercus petraea) is likely to spread in the context of current climate change and is increasingly planted in France. Seed sourcing is of the utmost importance for ensuring plantation success and adaptation. The selection of appropriate seed sources is highly challenging when the future climate conditions of plantation areas are uncertain. Aims We aimed at identifying drivers of provenance variation in Q. petraea and to build provenance clusters based on traits of adaptive and economic value, to ultimately support decision-making in seed sourcing. Methods We analysed a multisite provenance test established 30 years ago and comprising a large collection of Q. petraea provenances by performing phenotypic assessments of survival, growth, phenology, and stem-quality traits. We analysed climate-trait correlations at a range-wide scale and used multivariate statistics [multivariate mixed models, principal component analysis (PCA)] and classification methods [hierarchical clustering analysis (HCA), K-means method] to generate an overall clustering of french provenances. Results Provenance effects were highly significant regardless of the trait considered, whereas interaction effects between provenance and other experimental sources of variation were minor compared to provenance and environmental variance. There was limited variation between provenances collected in the same forest in comparison to origins of different forests. We found sharp temperature-driven genetic clines for growth and phenology-related traits at a range-wide scale. The multitrait classification approach grouped the French provenances into 11 clusters, with the members of each cluster having similar trait values. Overall, the cluster composition of provenances poorly matched the provenance regions identified on ecological grounds, but rather mirrored the silvicultural regimes implemented in the source stands in the past. Conclusions Two of the provenance clusters (comprising a total of 34 provenances) were identified as potentially useful sources of reproductive material. We recommend mixing seeds of different provenances from a given cluster to ensure the maintenance of diversity and to enhance adaptability to future climatic conditions

Exchangeable miniaturized mass spectrometer chip based on silicon structures

This paper reports a design of an exchangeable miniaturized mass spectrometry chip using spring-loaded pins and O-rings for electrical and fluidic connections. This planar microelectromechanical system (MEMS)-chip works with 300 $\mu$m high silicon structures between two borosilicate glasses and has a size of 13 mm × 7 mm. Because of its small size a small vacuum pump is sufficient, and it is suitable for mobile measurements and portable applications. Because of exchangeability of MEMS-chips with fluidic and electrical high voltage connections a direct comparison between chips is possible